[Biopython] Fwd: Some ideas to add functionalities to Bio.Blast

[Peter Cock]

On Sat, Sep 3, 2011 at 11:33 AM, Marco Galardini
<marco.galardini at unifi.it> wrote:
> Hi everybody,
>
> i'm sending to you this e-mail in order to see if the BioPython
> community may be interested in enhancing the features related to the
> Blast package: i've been using it for quite a long time now and over the
> months i've created a set of functions that may be useful to other
> scientists using Blast through the BioPython interface.
> To be a little more specific, it would be desirable to have some
> functions to build a database (makeblastdb), to retrieve sequences from
> a db (blastdbcmd),...

The Bio.Applications module is currently lacking wrappers for those,
so adding them would be very welcome:

https://github.com/biopython/biopython/blob/master/Bio/Blast/Applications.py

Could you sign up to the Biopython developers mailing list which
is were code contributions tend to be discussed. Thanks.

> to have some statistics from the overall blast run
> (average evalue, sequence identiy, ...) and most importantly some
> Classes to perform some specific analysis like Bi-directional Blast Hits
> (BBH) (which may be even genome-wide for comparative genomics purposes).
> Do you think that features like that may be useful/needed by the
> BioPython community? I would be really glad to give my contribution on
> that issues.

These later ideas are harder to generalise into library functions,
but if done well could be very widely used. I've written reciprocal
best hit BLAST code myself for example (as a Python script for
use in Galaxy). If you've got some code already written that
you'd like to share, please do so - even if we decide some of
it would be better as a Cookbook example rather than in the
core library, it would still be very useful to the community.

Regards,

Peter